cibuild.yml

name: CI Build

on: [push]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install
      run: |
        sudo apt-get update
        sudo apt-get install minimap2 samtools fastqc tabix
        curl -L -O http://ccb.jhu.edu/software/FLASH/FLASH-1.2.11-Linux-x86_64.tar.gz && tar -xzf FLASH-1.2.11-Linux-x86_64.tar.gz && sudo cp FLASH-1.2.11-Linux-x86_64/flash /usr/local/bin/ && rm -r FLASH-1.2.11*
        python -m pip install --upgrade pip
        pip install .
        mhpl8r getrefr
        make devdeps
    - name: Test with pytest
      run: |
        # Move the source code so the tests run on the *installed* code (which is where the
        # reference genome index is placed) rather than the source code
        mv microhapulator mhpl8r_src
        make test
        # Move the code back for style check
        mv mhpl8r_src microhapulator
    - name: Style check
      run: make style